mutation predictions | marginal predictions | summary statistics | genome diff | command line log
|
breseq version 0.39.0
mutation predictions | marginal predictions | summary statistics | genome diff | command line log |
| Predicted mutations | |||||
|---|---|---|---|---|---|
| evidence | position | mutation | annotation | gene | description |
| RA | 42,108 | G→A | intergenic (‑177/‑295) | caiT ← / → fixA | L‑carnitine:gamma‑butyrobetaine antiporter/putative electron transfer flavoprotein FixA |
| RA | 75,070 | C→T | P137P (CCG→CCA) | thiB ← | thiamine ABC transporter periplasmic binding protein |
| RA | 226,027 | C→T | noncoding (269/2904 nt) | rrlH → | 23S ribosomal RNA |
| RA | 232,736 | C→T | G407D (GGC→GAC) | mltD ← | membrane‑bound lytic murein transglycosylase D |
| RA | 233,353 | C→T | R201R (CGG→CGA) | mltD ← | membrane‑bound lytic murein transglycosylase D |
| RA | 236,201 | C→T | G45G (GGC→GGT) | dnaQ → | DNA polymerase III subunit epsilon |
| RA | 239,359 | C→T | intergenic (‑623/+60) | ykfM ← / ← yafV | uncharacterized protein YkfM/2‑oxoglutaramate amidase |
| RA | 239,412 | C→T | intergenic (‑676/+7) | ykfM ← / ← yafV | uncharacterized protein YkfM/2‑oxoglutaramate amidase |
| RA | 246,747 | G→T | S12S (TCG→TCT) | yafL → | NlpC/P60 family protein YafL |
| RA | 284,535 | T→G | A445A (GCT→GCG) | yagF → | D‑xylonate dehydratase |
| RA | 303,911 | C→T | G91E (GGA→GAA) | ykgJ ← | putative metal‑chelating domain‑containing protein YkgJ |
| RA | 313,543 | G→A | intergenic (‑301/‑1748) | ykgR ← / → insE1 | putative membrane protein YkgR/IS3 element protein InsE |
| RA | 330,640 | A→G | E393G (GAG→GGG) | betT → | choline:H(+) symporter |
| RA | 331,446 | C→T | H662Y (CAT→TAT) | betT → | choline:H(+) symporter |
| RA | 334,180 | C→T | R85K (AGA→AAA) | yahB ← | putative LysR‑type DNA‑binding transcriptional regulator YahB |
| RA | 335,016 | C→T | G3R (GGA→AGA) | yahC ← | uncharacterized protein YahC |
| RA | 431,730 | C→T | G95D (GGT→GAT) | tsx ← | nucleoside‑specific channel‑forming protein Tsx |
| RA | 438,659 | C→T | A507T (GCG→ACG) | dxs ← | 1‑deoxy‑D‑xylulose‑5‑phosphate synthase |
| RA | 457,365 | C→T | intergenic (+65/‑61) | clpP → / → clpX | ATP‑dependent Clp protease proteolytic subunit/ATP‑dependent Clp protease ATP‑binding subunit ClpX |
| RA | 462,067 | C→T | S51S (AGC→AGT) | ppiD → | periplasmic folding chaperone |
| RA | 465,894 | C→T | E473E (GAG→GAA) | ybaE ← | uncharacterized protein YbaE |
| RA | 472,159 | C→T | D508D (GAC→GAT) | mdlB → | ABC transporter family protein MdlB |
| RA | 473,963 | C→T | P333L (CCC→CTC) | amtB → | ammonium transporter |
| RA | 476,337 | C→T | G12D (GGC→GAC) | ybaZ ← | DNA base‑flipping protein |
| RA | 478,372 | C→T | M82I (ATG→ATA) | pdeB ← | c‑di‑GMP phosphodiesterase PdeB |
| RA | 480,295 | 2 bp→AA | coding (13‑14/219 nt) | hha ← | hemolysin expression‑modulating protein Hha |
| RA | 484,026 | C→T | G126G (GGG→GGA) | acrB ← | multidrug efflux pump RND permease AcrB |
| RA | 487,341 | C→T | A269V (GCG→GTG) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 488,403 | C→T | T623I (ACC→ATC) | mscK → | potassium dependent, small conductance mechanosensitive channel |
| RA | 492,768 | C→T | A226V (GCC→GTC) A226V (GCC→GTC) |
dnaX → dnaX → |
DNA polymerase III subunit tau DNA polymerase III subunit tau |
| RA | 495,622 | C→T | T168I (ACC→ATC) | htpG → | chaperone protein HtpG |
| RA | 505,779 | A→C | H289P (CAT→CCT) | ushA → | 5'‑nucleotidase/UDP‑sugar hydrolase |
| RA | 696,470 | C→T | noncoding (35/75 nt) | glnX ← | tRNA‑Gln |
| RA | 880,964 | C→T | L80F (CTT→TTT) | dacC → | D‑alanyl‑D‑alanine carboxypeptidase DacC |
| RA | 1,001,251 | A→C | Q679P (CAA→CCA) | elfC → | putative fimbrial usher protein ElfC |
| RA | 1,148,972 | C→T | Q72* (CAG→TAG) | fabH → | 3‑oxoacyl‑[acyl carrier protein] synthase 3 |
| RA | 1,169,836 | A→G | L180P (CTG→CCG) | ldtC ← | L,D‑transpeptidase LdtC |
| RA | 1,189,980 | A→G | T156T (ACT→ACC) | phoP ← | DNA‑binding transcriptional dual regulator PhoP |
| RA | 1,287,040 | G→A | intergenic (+56/+26) | ychS → / ← rttR | putative uncharacterized protein YchS/small RNA RttR |
| MC JC | 1,299,499 | Δ1,199 bp | insH21 | insH21 | |
| RA | 1,301,992 | A→T | N271Y (AAT→TAT) | oppA → | oligopeptide ABC transporter periplasmic binding protein |
| RA | 1,336,674 | G→A | G282R (GGG→AGG) | acnA → | aconitate hydratase 1 |
| RA | 1,337,394 | A→G | S522G (AGC→GGC) | acnA → | aconitate hydratase 1 |
| RA | 1,339,315 | C→T | intergenic (‑155/‑15) | ribA ← / → pgpB | GTP cyclohydrolase 2/phosphatidylglycerophosphatase B |
| RA | 1,350,005 | C→T | V35I (GTC→ATC) | yciW ← | putative peroxidase YciW |
| RA | 1,358,859 | T→C | Y110C (TAT→TGT) | puuP ← | putrescine:H(+) symporter PuuP |
| RA | 1,600,491 | C→A | A251S (GCA→TCA) | lsrR ← | DNA‑binding transcriptional repressor LsrR |
| RA | 1,643,679 | A→T | L209Q (CTG→CAG) | ydfU ← | protein YdfU |
| RA | 1,652,331 | T→C | intergenic (+2346/+397) | ydfD → / ← ynfP | lysis protein/protein YnfP |
| RA | 1,829,887 | G→A | A293A (GCC→GCT) | astA ← | arginine N‑succinyltransferase |
| RA | 1,894,839 | T→C | L12P (CTC→CCC) | pabB → | aminodeoxychorismate synthase subunit 1 |
| RA | 1,894,969 | C→T | C55C (TGC→TGT) | pabB → | aminodeoxychorismate synthase subunit 1 |
| MC JC | 1,978,503 | Δ776 bp | insB5–insA5 | insB5, insA5 | |
| JC JC | 1,979,518 | IS5 (+) +4 bp | intergenic (‑303/‑232) | insA5 ← / → uspC | IS1 family protein InsA/universal stress protein C |
| RA | 2,000,331 | G→A | L19L (CTG→TTG) | tcyJ ← | cystine ABC transporter periplasmic binding protein |
| RA | 2,040,433 | C→A | A319D (GCC→GAC) | msrP → | protein‑L‑methionine sulfoxide reductase catalytic subunit MsrP |
| RA | 2,041,827 | T→C | C151C (TGT→TGC) | zinT → | metal‑binding protein ZinT |
| RA | 2,042,171 | G→A | intergenic (+146/‑197) | zinT → / → yodB | metal‑binding protein ZinT/putative cytochrome b561 YodB |
| RA | 2,044,642 | T→C | intergenic (+18/‑296) | asnT → / → yeeJ | tRNA‑Asn/inverse autotransporter adhesin |
| RA | 2,051,845 | G→A | W2303* (TGG→TAG) | yeeJ → | inverse autotransporter adhesin |
| RA | 2,111,259 | Δ1 bp | coding (718/900 nt) | rfbD ← | dTDP‑4‑dehydrorhamnose reductase |
| RA | 2,177,346 | G→A | intergenic (‑142/+166) | gatY ← / ← fbaB | tagatose‑1,6‑bisphosphate aldolase 2/fructose‑bisphosphate aldolase class I |
| RA | 2,222,148 | G→A | intergenic (‑159/‑37) | bglX ← / → dld | beta‑D‑glucoside glucohydrolase, periplasmic/quinone‑dependent D‑lactate dehydrogenase |
| RA | 2,227,397 | G→A | intergenic (‑127/‑1585) | yohF ← / → yohP | putative oxidoreductase YohF/putative membrane protein YohP |
| RA | 2,291,674 | G→A | A246V (GCC→GTC) | ccmH ← | holocytochrome c synthase CcmH component |
| RA | 2,323,558 | G→A | A38T (GCA→ACA) | atoD → | acetyl‑CoA:acetoacetyl‑CoA transferase subunit alpha |
| RA | 2,333,124 | G→A | intergenic (‑3327/+1212) | yfaQ ← / ← yfaT | tandem DUF2300 domain‑containing protein YfaQ/DUF1175 domain‑containing protein YfaT |
| RA | 2,337,998 | G→A | L475F (CTC→TTC) | gyrA ← | DNA gyrase subunit A |
| RA | 2,361,249 | G→A | Q56* (CAG→TAG) | rhmD ← | L‑rhamnonate dehydratase |
| RA | 2,395,340 | G→A | I2I (ATC→ATT) | nuoK ← | NADH:quinone oxidoreductase subunit K |
| RA | 2,411,035 | G→A | G106G (GGC→GGT) | yfbS ← | putative transporter YfbS |
| RA | 2,434,316 | G→A | A142A (GCC→GCT) | dedA ← | DedA family protein DedA |
| RA | 2,435,632 | G→A | S2F (TCC→TTC) | truA ← | tRNA pseudouridine(38‑40) synthase |
| JC JC | 2,468,298 | IS3 (+) +3 bp | coding (85‑87/921 nt) | yfdH → | bactoprenol glucosyl transferase |
| MC JC | 2,558,699 | Δ6,790 bp | intZ–[eutA] | intZ, yffL, yffM, yffN, yffO, yffP, yffQ, yffR, yffS, [eutA] | |
| RA | 2,587,112 | C→T | A461V (GCA→GTA) | narQ → | sensor histidine kinase NarQ |
| JC JC | 2,620,645 | IS1 (+) +9 bp | coding (220‑228/627 nt) | upp ← | uracil phosphoribosyltransferase |
| RA | 2,756,356 | C→T | V66V (GTC→GTT) | intA → | integrase IntA |
| RA | 2,834,329 | G→A | D140N (GAT→AAT) | norW → | NADH:flavorubredoxin reductase |
| RA | 2,867,455 | G→A | Q33* (CAG→TAG) | rpoS ← | RNA polymerase sigma factor RpoS |
| RA | 2,926,772 | C→A | G155G (GGC→GGA) | ppnN → | nucleotide 5'‑monophosphate nucleosidase |
| RA | 2,949,623 | G→A | V128I (GTC→ATC) | argA → | N‑acetylglutamate synthase |
| RA | 3,042,536 | T→C | S205G (AGT→GGT) | yqfA ← | hemolysin‑III family protein YqfA |
| RA | 3,152,494 | G→T | A87S (GCG→TCG) | metC → | cystathionine beta‑lyase/L‑cysteine desulfhydrase/alanine racemase |
| RA | 3,207,549 | Δ1 bp | coding (179/606 nt) | ttdB → | L(+)‑tartrate dehydratase subunit beta |
| RA | 3,329,743 | G→T | D261Y (GAT→TAT) | dacB → | peptidoglycan DD‑endopeptidase DacB |
| RA | 3,388,041 | T→G | T50P (ACG→CCG) | aaeB ← | aromatic carboxylic acid efflux pump subunit AaeB |
| JC JC | 3,429,986 | IS3 (–) +5 bp :: +T | coding (34‑38/258 nt) | yrdB ← | DUF1488 domain‑containing protein YrdB |
| RA | 3,474,425 | T→G | K43T (AAA→ACA) | rpsL ← | 30S ribosomal subunit protein S12 |
| RA | 3,560,443 | C→G | intergenic (+577/+179) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,560,455 | +G | intergenic (+589/+167) | rtcR → / ← glpG | DNA‑binding transcriptional activator RtcR/rhomboid protease GlpG |
| RA | 3,667,950 | G→A | Y413Y (TAC→TAT) | ccp ← | cytochrome c peroxidase |
| RA | 3,707,883 | G→A | intergenic (‑178/+733) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,707,947 | C→A | intergenic (‑242/+669) | dppA ← / ← proK | dipeptide ABC transporter periplasmic binding protein/tRNA‑Pro |
| RA | 3,725,176 | T→G | E48A (GAG→GCG) | glyQ ← | glycine‑‑tRNA ligase subunit alpha |
| RA | 3,815,883 | +C | coding (667/687 nt) | rph ← | truncated RNase PH |
| RA | 3,964,675 | C→T | G319D (GGT→GAT) | rhlB ← | ATP‑dependent RNA helicase RhlB |
| RA | 3,973,874 | C→T | A89A (GCC→GCT) | rffH → | glucose‑1‑phosphate thymidylyltransferase 2 |
| RA | 4,000,353 | C→T | G235E (GGG→GAG) | yigE ← | DUF2233 domain‑containing protein YigE |
| RA | 4,024,199 | C→T | P216S (CCA→TCA) | tatD → | 3' ‑> 5' ssDNA/RNA exonuclease TatD |
| RA | 4,067,555 | C→T | E574E (GAG→GAA) | yihQ ← | sulfoquinovosidase |
| RA | 4,074,275 | C→T | A179A (GCC→GCT) | yihV → | 6‑deoxy‑6‑sulfofructose kinase |
| RA | 4,109,671 | C→T | R280C (CGT→TGT) | sbp → | sulfate/thiosulfate ABC transporter periplasmic binding protein Sbp |
| RA | 4,159,997 | A→T | L265Q (CTG→CAG) | sthA ← | soluble pyridine nucleotide transhydrogenase |
| RA | 4,180,421 | C→T | T142T (ACC→ACT) | rplJ → | 50S ribosomal subunit protein L10 |
| RA | 4,193,996 | T→G | D70A (GAT→GCT) | thiE ← | thiamine phosphate synthase |
| RA | 4,223,638 | T→C | intergenic (‑10/‑190) | iclR ← / → metH | DNA‑binding transcriptional repressor IclR/cobalamin‑dependent methionine synthase |
| RA | 4,287,464 | T→A | intergenic (‑93/‑147) | acs ← / → ytcB | acetyl‑CoA synthetase (AMP‑forming)/protein YtcB |
| RA | 4,296,381 | +GC | intergenic (+587/+55) | gltP → / ← yjcO | glutamate/aspartate : H(+) symporter GltP/Sel1 repeat‑containing protein YjcO |
| RA | 4,325,644 | C→T | S33N (AGC→AAC) | yjdN ← | PF06983 family protein YjdN |
| RA | 4,473,900 | C→T | G52R (GGA→AGA) | bdcA ← | c‑di‑GMP‑binding biofilm dispersal mediator protein |
| RA | 4,475,493 | T→C | F19F (TTT→TTC) | yjgL → | protein YjgL |
| RA | 4,510,238 | T→G | intergenic (+445/+452) | insO → / ← fecE | IS911B regulator fragment/ferric citrate ABC transporter ATP binding subunit |
| RA | 4,531,415 | C→T | E79E (GAG→GAA) | sgcX ← | putative endoglucanase with Zn‑dependent exopeptidase domain |
| JC JC | 4,542,042 | IS1 (+) +8 bp | coding (6‑13/597 nt) | fimE → | regulator for fimA |
| RA | 4,563,778 | (G)6→5 | coding (148/258 nt) | ytiA ← | uncharacterized protein YtiA |
| RA | 4,575,319 | C→T | intergenic (+1388/+1593) | yjiT → / ← mcrC | putative uncharacterized protein YjiT/Type IV methyl‑directed restriction enzyme EcoKMcrBC subunit |
| RA | 4,580,552 | C→T | G304E (GGG→GAG) | hsdS ← | type I restriction enzyme EcoKI specificity subunit |
| RA | 4,583,800 | C→T | D988N (GAC→AAC) | hsdR ← | type I restriction enzyme EcoKI endonuclease subunit |
| RA | 4,593,035 | C→T | A460V (GCT→GTT) | tsr → | methyl‑accepting chemotaxis protein Tsr |
| RA | 4,615,345 | C→T | G67S (GGC→AGC) | yjjW ← | putative glycyl‑radical enzyme activating enzyme YjjW |
| RA | 4,627,820 | G→A | G169E (GGG→GAG) | nadR → | DNA‑binding transcriptional repressor/NMN adenylyltransferase NadR |
| RA | 4,636,925 | G→C | R77P (CGC→CCC) | creC → | sensory histidine kinase CreC |
| RA | 4,638,240 | G→A | L21L (TTG→TTA) | creD → | putative inner membrane protein CreD |
| Unassigned missing coverage evidence | ||||||||||
|---|---|---|---|---|---|---|---|---|---|---|
| seq id | start | end | size | ←reads | reads→ | gene | description | |||
| * | * | ÷ | NC_000913 | 168355 | 168703 | 349 | 38 [0] | [0] 34 | fhuA | ferrichrome outer membrane transporter/phage receptor |
| * | * | ÷ | NC_000913 | 182573 | 182988 | 416 | 2 [1] | [0] 34 | cdaR | DNA‑binding transcriptional activator CdaR |
| * | * | ÷ | NC_000913 | 258135–258672 | 258676 | 5–542 | 2 [0] | [1] 2 | [insB9]–[crl] | [insB9],insA9,[crl] |
| * | * | ÷ | NC_000913 | 402391 | 403109 | 719 | 11 [0] | [1] 2 | phoA | alkaline phosphatase |
| * | * | ÷ | NC_000913 | 1632293 | 1632318 | 26 | 2 [1] | [1] 2 | ydfJ/ynfT | putative transporter YdfJ/protein YnfT |
| * | * | ÷ | NC_000913 | 1669533 | 1669586 | 54 | 4 [1] | [1] 2 | ynfL | putative DNA‑binding transcriptional regulator YnfL |
| * | * | ÷ | NC_000913 | 2168157 | 2177242 | 9086 | 23 [0] | [0] 22 | [yegR]–gatY | [yegR],yegS,gatR,insE5,insF5,gatR,gatD,gatB,gatA,gatZ,gatY |
| * | * | ÷ | NC_000913 | 3423880–3424232 | 3424412–3424239 | 8–533 | 2 [1] | [1] 3 | rrlD | 23S ribosomal RNA |
| * | * | ÷ | NC_000913 | 4035417–4035688 | 4036867–4035736 | 49–1451 | 3 [1] | [1] 2 | [rrsA] | [rrsA] |
| Unassigned new junction evidence | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
| seq id | position | reads (cov) | reads (cov) | score | skew | freq | annotation | gene | product | ||
| * | ? | NC_000913 | = 168354 | 0 (0.000) | 37 (1.530) | 37/470 | 0.0 | 100% | coding (871/2244 nt) | fhuA | ferrichrome outer membrane transporter/phage receptor |
| ? | NC_000913 | = 182568 | 0 (0.000) | coding (106/1158 nt) | cdaR | DNA‑binding transcriptional activator CdaR | |||||
| * | ? | NC_000913 | 168704 = | 0 (0.000) | 34 (1.390) | 31/476 | 0.1 | 100% | coding (1221/2244 nt) | fhuA | ferrichrome outer membrane transporter/phage receptor |
| ? | NC_000913 | 182989 = | 0 (0.000) | coding (527/1158 nt) | cdaR | DNA‑binding transcriptional activator CdaR | |||||
| * | ? | NC_000913 | = 257907 | 2 (0.080) | 24 (0.980) | 21/476 | 0.3 | 96.1% | intergenic (+8/+16) | crl/insB9 | RNA polymerase holoenzyme assembly factor Crl/IS1 family transposase B |
| ? | NC_000913 | 258684 = | 0 (0.000) | pseudogene (9/331 nt) | crl | RNA polymerase holoenzyme assembly factor Crl | |||||
| * | ? | NC_000913 | = 402390 | 0 (0.000) | 11 (0.440) | 10/482 | 0.8 | 95.7% | coding (644/1416 nt) | phoA | alkaline phosphatase |
| ? | NC_000913 | 403114 = | 1 (0.040) | coding (1368/1416 nt) | phoA | alkaline phosphatase | |||||
| * | ? | NC_000913 | 1207790 = | 6 (0.240) | 6 (0.250) | 6/460 | 1.2 | 55.5% | coding (290/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | 1209619 = | 4 (0.170) | intergenic (‑500/‑66) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | = 1207805 | 6 (0.240) | 3 (0.130) | 3/460 | 1.8 | 38.4% | coding (305/630 nt) | ycfK | protein StfP |
| ? | NC_000913 | = 1209602 | 4 (0.170) | intergenic (‑483/‑83) | tfaE/pinE | putative tail fiber assembly protein TfaE/site‑specific DNA recombinase | |||||
| * | ? | NC_000913 | 1978503 = | NA (NA) | 22 (0.880) | 22/488 | 0.2 | 100% | noncoding (768/768 nt) | IS1 | repeat region |
| ? | NC_000913 | = 2168156 | 0 (0.000) | coding (151/318 nt) | yegR | uncharacterized protein YegR | |||||
| * | ? | NC_000913 | = 1979270 | NA (NA) | 21 (0.830) | 21/492 | 0.3 | 100% | noncoding (1/768 nt) | IS1 | repeat region |
| ? | NC_000913 | 2177243 = | 0 (0.000) | intergenic (‑39/+269) | gatY/fbaB | tagatose‑1,6‑bisphosphate aldolase 2/fructose‑bisphosphate aldolase class I | |||||
| * | ? | NC_000913 | 2288919 = | NA (NA) | 13 (0.520) | 13/488 | 0.6 | 61.9% | noncoding (1195/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | 3727274 = | 8 (0.320) | coding (88/438 nt) | yiaA | PF05360 family inner membrane protein YiaA | |||||
| * | ? | NC_000913 | = 2290113 | NA (NA) | 8 (0.320) | 8/492 | 1.1 | 50.0% | noncoding (1/1195 nt) | IS5 | repeat region |
| ? | NC_000913 | = 3727277 | 8 (0.320) | coding (85/438 nt) | yiaA | PF05360 family inner membrane protein YiaA | |||||
| * | ? | NC_000913 | 4542682 = | 10 (0.400) | 6 (0.250) | 6/474 | 1.3 | 33.7% | intergenic (+49/‑433) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | 4542996 = | 14 (0.570) | intergenic (+363/‑119) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||
| * | ? | NC_000913 | = 4542690 | 11 (0.430) | 8 (0.330) | 7/474 | 1.1 | 39.4% | intergenic (+57/‑425) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit |
| ? | NC_000913 | = 4542986 | 14 (0.570) | intergenic (+353/‑129) | fimE/fimA | regulator for fimA/type 1 fimbriae major subunit | |||||